The pair finished behind Great Britain in the women's B 3000m Individual Pursuit.
New Zealand's newest tandem pairing of Amanda Cameron and Hannah van Kampen finished fourth.
Foy, who only entered the sport of para-cycling just over three years ago, is joined by sighted pilot Thompson who brings extensive Paralympic Games experience after winning the trifecta of medals at London 2012.
Para-cycling was about team work with pilot Laura Thompson, Foy told Morning Report